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Most grasses host endophytic fungi, co-evolved organisms that can interact with their hosts from antagonism to mutualism. This study examined the impact of mating systems on host–endophyte interactions by utilizing endophyte-infected (E+) and endophyte-free (E−) populations of self-pollinating Lolium persicum and open-pollinating Lolium rigidum, collected from three regions of Iran. The evaluations in a pre-breeding process and two experiments were conducted on 1400 plants screened to select 126 half-sib (L. rigidum) and full-sib (L. persicum) families based on a limited space stress, morphological traits, and seed dormancy, respectively. It was found that endophytes generally have a significant and positive effect on reproductive traits and promoting effects in plants to strive for survival. Their impacts were population-dependent, and the E+ plants were superior when a population had higher biomass production and seed yield-related traits. Endophytes help to maintain the host’s genetic structure over generations, particularly in L. persicum. In this way, E+ populations exhibited the highest heritability and genetic advance for endophyte–host survival traits such as seed weight, number of seeds, plant height, and days to tillering in both species. In L. persicum, this also included acid-detergent fiber, neutral detergent fiber, crude protein, fat content, phosphorus content, number of tillers, and days to emergence. We demonstrated that artificial selection of morphological traits influenced plant–fungal fitness, such that selecting against seed dormancy significantly increased seed shattering but decreased fungal fitness.